Phil Jones, the beleaguered British climate scientist at the centre of the leaked emails controversy, is facing fresh claims that he sought to hide problems in key temperature data on which some of his work was based.

A Guardian investigation of thousands of emails and documents apparently hacked from the University of East Anglia's climatic research unit has found evidence that a series of measurements from Chinese weather stations were seriously flawed and that documents relating to them could not be produced.

Jones and a collaborator have been accused by a climate change sceptic and researcher of scientific fraud for attempting to suppress data that could cast doubt on a key 1990 study on the effect of cities on warming – a hotly contested issue.

Today the Guardian reveals how Jones withheld the information requested under freedom of information laws. Subsequently a senior colleague told him he feared that Jones's collaborator, Wei-­Chyung Wang of the University at Albany, had "screwed up".

The revelations on the inadequacies of the 1990 paper do not undermine the case that humans are causing climate change, and other studies have produced similar findings. But they do call into question the probity of some climate change science.

The apparent attempts to cover up problems with temperature data from the Chinese weather stations provide the first link between the email scandal and the UN's embattled climate science body, the Intergovernmental Panel on Climate Change, as a paper based on the measurements was used to bolster IPCC statements about rapid global warming in recent decades.

Wang was cleared of scientific fraud by his university, but new information brought to light today indicates at least one senior colleague had serious concerns about the affair.

It also emerges that documents which Wang claimed would exonerate him and Jones did not exist.

The revelations come at a torrid time for climate science, with the IPPC suffering heavy criticism for its use of information that had not been rigorously checked – in particular a false claim that all Himalayan glaciers could melt by 2035 – and UEA having been criticised last week by the deputy information commissioner for refusing valid requests for data under the Freedom of Information Act.

The Guardian has learned that of 105 freedom of information requests to the university concerning the climatic research unit (CRU), which Jones headed up to the end of December, only 10 had been released in full.

The temperature data from the Chinese weather stations measured the warming there over the past half century and appeared in a 1990 paper in the prestigious journal Nature, which was cited by the IPCC's latest report in 2007.

Climate change sceptics asked the UEA, via FOI requests, for location data for the 84 weather stations in eastern China, half of which were urban and half rural.

The history of where the weather stations were sited was crucial to Jones and Wang's 1990 study, as it concluded the rising temperatures recorded in China were the result of global climate changes rather the warming effects of expanding cities.

The IPCC's 2007 report used the study to justify the claim that "any urban-related trend" in global temperatures was small. Jones was one of two "coordinating lead authors" for the relevant chapter.

The leaked emails from the CRU reveal that the former director of the unit, Tom Wigley, harboured grave doubts about the cover-up of the shortcomings in Jones and Wang's work. Wigley was in charge of CRU when the original paper was published. "Were you taking W-CW [Wang] on trust?" he asked Jones. He continued: "Why, why, why did you and W-CW not simply say this right at the start?"

Jones said he was not able to comment on the story.

Wang said: "I have been exonerated by my university on all the charges. When we started on the paper we had all the station location details in order to identify our network, but we cannot find them any more.

"Some of the location changes were probably only a few metres, and where they were more we corrected for them."

In an interview with the Observer on Sunday Ed Miliband, the climate change secretary, warned of the danger of a public backlash against mainstream climate science over claims that scientists manipulated data. He declared a "battle" against the "siren voices" who denied global warming was real or caused by humans. "It's right that there's rigour applied to all the reports about climate change, but I think it would be wrong that when a mistake is made it's somehow used to undermine the overwhelming picture that's there," he said.

Last week the Information Commissioner's Office – the body that administers the Freedom of Information Act – said the University of East Anglia had flouted the rules in its handling of an FOI request in May 2008.